Difference between revisions of "Locations of best sites (analysis)"
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==== Parameters: ==== | ==== Parameters: ==== | ||
| + | * '''Input track''' – Select input track (it can be ChIP-seq track from GTRD; thus, it can be the result of MACS or SISSRs peak-finder) | ||
* '''Sequences collection''' – Select a source of nucleotide sequences | * '''Sequences collection''' – Select a source of nucleotide sequences | ||
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually | ** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually | ||
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected | ** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected | ||
| − | |||
* '''Is around summit''' – Is around summit | * '''Is around summit''' – Is around summit | ||
* '''Minimal region length''' – Minimal length of sequence region | * '''Minimal region length''' – Minimal length of sequence region | ||
| − | * '''Matrix''' – Path to | + | * '''Types of site models''' – Select site models for comparative analysis |
| − | * ''' | + | * '''Matrix''' – Path to frequency matrix |
| + | * '''Path to output folder''' – Output folder will be created under this location when it doesn<nowiki>'</nowiki>t exist | ||
[[Category:Analyses]] | [[Category:Analyses]] | ||
Latest revision as of 19:00, 13 February 2017
- Analysis title
Locations of best sites
- Provider
- Institute of Systems Biology
- Class
BestSiteLocations- Plugin
- biouml.plugins.bindingregions (Binding-regions related analyses)
[edit] Description
Best sites: location of best sites in single chip-seq track; summit(yes/no)
[edit] Parameters:
- Input track – Select input track (it can be ChIP-seq track from GTRD; thus, it can be the result of MACS or SISSRs peak-finder)
- Sequences collection – Select a source of nucleotide sequences
- Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
- Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
- Is around summit – Is around summit
- Minimal region length – Minimal length of sequence region
- Types of site models – Select site models for comparative analysis
- Matrix – Path to frequency matrix
- Path to output folder – Output folder will be created under this location when it doesn't exist
